Introduce strict shell command option.

Newer tool formats (CWL and YAML just enable this by default), but XML tools can add a strict="true" to the command block to force "set -e" handling on the shell part of tool execution.

Run the framework tests verifying the new and older default behavior using the following commands:

```
./run_tests.sh -framework -id strict_shell_default_off
./run_tests.sh -framework -id strict_shell
```

lib/galaxy/jobs/__init__.py

@@ -793,6 +793,10 @@ class JobWrapper( object ):
     def shell(self):
         return self.job_destination.shell or getattr(self.app.config, 'default_job_shell', DEFAULT_JOB_SHELL)
 
+    @property
+    def strict_shell(self):
+        return self.tool.strict_shell
+
     @property
     def commands_in_new_shell(self):
         return self.app.config.commands_in_new_shell

lib/galaxy/jobs/command_factory.py

@@ -87,7 +87,15 @@ def __externalize_commands(job_wrapper, shell, commands_builder, remote_command_
     integrity_injection = ""
     if check_script_integrity(config):
         integrity_injection = INTEGRITY_INJECTION
-    script_contents = u"#!%s\n%s%s" % (shell, integrity_injection, tool_commands)
+    set_e = ""
+    if job_wrapper.strict_shell:
+        set_e = "set -e\n"
+    script_contents = u"#!%s\n%s%s%s" % (
+        shell,
+        integrity_injection,
+        set_e,
+        tool_commands
+    )
     write_script(local_container_script, script_contents, config)
     commands = local_container_script
     if 'working_directory' in remote_command_params:

lib/galaxy/tools/__init__.py

@@ -562,6 +562,9 @@ class Tool( object, Dictifiable ):
 
         # Parse result handling for tool exit codes and stdout/stderr messages:
         self.parse_stdio( tool_source )
+
+        self.strict_shell = tool_source.parse_strict_shell()
+
         # Any extra generated config files for the tool
         self.__parse_config_files(tool_source)
         # Action

lib/galaxy/tools/parser/cwl.py

@@ -61,6 +61,9 @@ class CwlToolSource(ToolSource):
     def parse_help(self):
         return ""
 
+    def parse_strict_shell(self):
+        return True
+
     def parse_stdio(self):
         # TODO: remove duplication with YAML
         from galaxy.jobs.error_level import StdioErrorLevel

lib/galaxy/tools/parser/interface.py

@@ -139,6 +139,12 @@ class ToolSource(object):
         dictionaries for use by Tool.
         """
 
+    @abstractmethod
+    def parse_strict_shell(self):
+        """ Return True if tool commands should be executed with
+        set -e.
+        """
+
     @abstractmethod
     def parse_stdio(self):
         """ Builds lists of ToolStdioExitCode and ToolStdioRegex objects

lib/galaxy/tools/parser/xml.py

@@ -281,6 +281,13 @@ class XmlToolSource(ToolSource):
             parser = StdioParser(self.root)
             return parser.stdio_exit_codes, parser.stdio_regexes
 
+    def parse_strict_shell(self):
+        command_el = self._command_el
+        if command_el is not None:
+            return string_as_bool(command_el.get("strict", "False"))
+        else:
+            return False
+
     def parse_help(self):
         help_elem = self.root.find( 'help' )
         return help_elem.text if help_elem is not None else None

lib/galaxy/tools/parser/yaml.py

@@ -64,6 +64,10 @@ class YamlToolSource(ToolSource):
         page_source = YamlPageSource(self.root_dict.get("inputs", {}))
         return PagesSource([page_source])
 
+    def parse_strict_shell(self):
+        # TODO: Add ability to disable this.
+        return True
+
     def parse_stdio(self):
         return error_on_exit_code()
 

test/functional/tools/samples_tool_conf.xml

@@ -23,6 +23,8 @@
   <tool file="metadata.xml" />
   <tool file="metadata_bam.xml" />
   <tool file="metadata_bcf.xml" />
+  <tool file="strict_shell.xml" />
+  <tool file="strict_shell_default_off.xml" />
   <tool file="detect_errors_aggressive.xml" />
   <tool file="md5sum.xml" />
   <!--

test/functional/tools/strict_shell.xml

@@ -0,0 +1,23 @@
+<tool id="strict_shell" name="strict_shell" version="1.0.0">
+    <command strict="true" detect_errors="exit_code">
+        echo "Hello" > $out_file1
+        ; sh -c "exit $exit_code"
+        ; sh -c "exit 0"
+    </command>
+    <inputs>
+        <param name="exit_code" type="integer" value="0" label="exit code"/>
+    </inputs>
+    <outputs>
+        <data name="out_file1" />
+    </outputs>
+    <tests>
+        <test expect_exit_code="0" expect_failure="false">
+            <param name="exit_code" value="0" />
+        </test>
+        <test expect_exit_code="1" expect_failure="true">
+            <param name="exit_code" value="1" />
+        </test>
+    </tests>
+    <help>
+    </help>
+</tool>

test/functional/tools/strict_shell_default_off.xml

@@ -0,0 +1,20 @@
+<tool id="strict_shell_default_off" name="strict_shell_default_off" version="1.0.0">
+    <command detect_errors="exit_code">
+        echo "Hello" > $out_file1
+        ; sh -c "exit $exit_code"
+        ; sh -c "exit 0"
+    </command>
+    <inputs>
+        <param name="exit_code" type="integer" value="0" label="exit code"/>
+    </inputs>
+    <outputs>
+        <data name="out_file1" />
+    </outputs>
+    <tests>
+        <test expect_exit_code="0" expect_failure="false">
+            <param name="exit_code" value="1" />
+        </test>
+    </tests>
+    <help>
+    </help>
+</tool>

test/unit/jobs/test_command_factory.py

@@ -155,6 +155,7 @@ class TestCommandFactory(TestCase):
 class MockJobWrapper(object):
 
     def __init__(self, job_dir):
+        self.strict_shell = False
         self.write_version_cmd = None
         self.command_line = MOCK_COMMAND_LINE
         self.dependency_shell_commands = []